2006 650cc yamaha v-classic transmission shifting problems

Sounds like a bent shift fork. While accelerating you can feel the power cutting in and out quickly. The problem will get worse if you keep pushing 2nd gear till it slips. You can learn where (at what RPM) it wants to jump out and start shifting before it jumps out. The long term fix is opening the transmission and fixing the bent shift fork.

The problem is a bent shift fork. The repair is major surgery on the transmission. The entire engine comes apart just to get to the forks. Some special tools are required. The generic diagram below shows how the shift forks work.

yes. it sounds like you have a bad shift fork, and the dogs (little ears) on the first gear could be bad also...would have been nice if this happened at the end of the last season, instead of the beginning of a new season.

Any oil with the JASO MA motorcycle certification. 10w-40 for cold climate, 20w-50 for warm climate/touring. Do not use any oil that says Energy Conserving on the label. It will shorten the life of your wet clutch and transmission gears. Synthetic oil will help your bike run cooler and shift easier. You will need 4 quarts of oil , an oil filter, and a new aluminum sealing washer for the drain plug.

Any oil with a JASO MA motorcycle rating. 10w-40 for colder climate or 20w-50 hot climate. Never use any oil that says "Energy Conserving" on the label it will shorten the life of your wet clutch and transmission gears. Synthetic oil will run cooler and shift easier when hot.

the shift pattern is 1 down 4 up the 650 came with a 5 speed

Your description of the problem is classic for a bent shift fork. Call a couple dealers and get a base cost for the repairs. It would be best if you take the bike to a dealer and let them look at it to confirm my diagnosis and I think they will. A cost of $750 would not surprise me. The costly thing about changing a shift fork is that the engine comes out of the frame and then gets a complete tear down, both top end and bottom end. Now the fork can be changed out then engine / transmission re-assembly begins. This is not a recommended repair for the novice mechanic. Please rate my answer. Thanks.

Not really, unless there is a shift kit in there. Have a transmission shop check it out.